I have tried selecting many different menu items just for the sake of it and none work.
I suppose that you don't see the module on your front page, even though you set it to display on all pages right ?
NO, I do not have a special layout for the home page or any page for that matter. The cart module is displayed on all pages / all menu items. Cart Module IS on the front page. You will see that if you were to visit the URL provided. Here it is again;
theuncommonlife.com/store/
Main menu is also set to show on all pages. I only have one layout, one template.
This strange menu disappearance only just started happening around the time I upgraded (after you added voting and comments)
I hope there could some some explanation, thank you for you help.
Jessica